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3PEF
Asym. Unit
Info
Asym.Unit (734 KB)
Biol.Unit 1 (363 KB)
Biol.Unit 2 (364 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GAMMA-HYDROXYBUTYRATE DEHYDROGENASE FROM GEOBACTER METALLIREDUCENS IN COMPLEX WITH NADP+
Authors
:
Y. Zhang, R. M. Garavito
Date
:
26 Oct 10 (Deposition) - 07 Dec 11 (Release) - 01 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.07
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Gamma-Hydroxybutyrate Dehydrogenase, Succinic Semialdehyde Reductase, Geobacter Metallireducens, Nadp+, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhang, Y. Zheng, L. Qin, S. Wang, G. W. Buchko, R. M. Garavito
Structural Characterization Of A Beta-Hydroxyacid Dehydrogenase From Geobacter Sulfurreducens And Geobacter Metallireducens With Succinic Semialdehyde Reductase Activity.
Biochimie V. 104 61 2014
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Hetero Components
(5, 29)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
1b: S-HYDROXYCYSTEINE (CSOb)
1c: S-HYDROXYCYSTEINE (CSOc)
1d: S-HYDROXYCYSTEINE (CSOd)
1e: S-HYDROXYCYSTEINE (CSOe)
1f: S-HYDROXYCYSTEINE (CSOf)
1g: S-HYDROXYCYSTEINE (CSOg)
1h: S-HYDROXYCYSTEINE (CSOh)
2a: 1,2-ETHANEDIOL (EDOa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
4a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
4b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
4c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
4d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
4e: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPe)
4f: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPf)
4g: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPg)
4h: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPh)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
5e: DI(HYDROXYETHYL)ETHER (PEGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
8
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
7
Ligand/Ion
GLYCEROL
4
NAP
8
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
5
PEG
5
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
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Sites
(21, 21)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:9 , GLY A:10 , ILE A:11 , MET A:12 , ASN A:31 , ARG A:32 , SER A:33 , LYS A:36 , MET A:64 , LEU A:65 , ALA A:66 , ALA A:70 , GLU A:73 , VAL A:74 , THR A:96 , VAL A:121 , GLY A:123 , SER A:124 , ALA A:231 , PHE A:232 , PRO A:233 , HIS A:236 , LYS A:239 , GOL A:288 , HOH A:296 , HOH A:315 , HOH A:333 , HOH A:343 , HOH A:362 , HOH A:456 , HOH A:572 , HOH A:1002
BINDING SITE FOR RESIDUE NAP A 301
02
AC2
SOFTWARE
GLY A:123 , SER A:124 , LYS A:171 , ASN A:175 , MET A:178 , PHE A:232 , NAP A:301 , HOH A:479 , HOH A:572 , HOH A:635 , HOH A:693
BINDING SITE FOR RESIDUE GOL A 288
03
AC3
SOFTWARE
ASP A:67 , LYS A:235 , HIS A:236 , LYS A:239 , ARG A:242 , ARG A:269
BINDING SITE FOR RESIDUE GOL A 289
04
AC4
SOFTWARE
LEU A:203 , GLY A:207 , ALA A:212 , ASN A:213 , PHE A:216 , ALA A:217
BINDING SITE FOR RESIDUE GOL A 290
05
AC5
SOFTWARE
ALA A:246 , ASP A:249 , HOH A:307 , ARG D:242 , HOH D:311 , HOH D:476
BINDING SITE FOR RESIDUE PEG A 291
06
AC6
SOFTWARE
GLY A:106 , VAL A:110 , PHE A:116 , VAL A:164 , HOH A:293 , HOH A:429 , HOH A:662 , HOH A:701
BINDING SITE FOR RESIDUE EDO A 292
07
AC7
SOFTWARE
LEU B:9 , GLY B:10 , ILE B:11 , MET B:12 , ASN B:31 , ARG B:32 , SER B:33 , MET B:64 , LEU B:65 , ALA B:66 , ALA B:70 , GLU B:73 , VAL B:74 , THR B:96 , VAL B:121 , GLY B:123 , SER B:124 , ALA B:231 , PHE B:232 , PRO B:233 , HIS B:236 , LYS B:239 , HOH B:311 , HOH B:393 , HOH B:500 , HOH B:613 , HOH B:626
BINDING SITE FOR RESIDUE NAP B 301
08
AC8
SOFTWARE
ARG B:141 , NAP G:301 , HOH G:493 , HOH G:638
BINDING SITE FOR RESIDUE GOL B 288
09
AC9
SOFTWARE
LEU C:9 , GLY C:10 , ILE C:11 , MET C:12 , ASN C:31 , ARG C:32 , SER C:33 , LYS C:36 , MET C:64 , LEU C:65 , ALA C:66 , ALA C:70 , GLU C:73 , VAL C:74 , THR C:96 , VAL C:121 , GLY C:123 , SER C:124 , ALA C:231 , PHE C:232 , PRO C:233 , HIS C:236 , LYS C:239 , GOL C:288 , HOH C:308 , HOH C:317 , HOH C:445 , HOH C:450 , HOH C:465 , HOH C:582
BINDING SITE FOR RESIDUE NAP C 301
10
BC1
SOFTWARE
GLY C:123 , SER C:124 , LYS C:171 , ASN C:175 , MET C:178 , PHE C:232 , NAP C:301
BINDING SITE FOR RESIDUE GOL C 288
11
BC2
SOFTWARE
LEU D:9 , GLY D:10 , ILE D:11 , MET D:12 , ASN D:31 , ARG D:32 , SER D:33 , MET D:64 , LEU D:65 , ALA D:66 , ALA D:70 , GLU D:73 , VAL D:74 , THR D:96 , VAL D:121 , GLY D:123 , SER D:124 , ALA D:231 , PHE D:232 , PRO D:233 , HIS D:236 , LYS D:239 , HOH D:303 , HOH D:321 , HOH D:324 , HOH D:334 , HOH D:584 , HOH D:586 , HOH D:730 , HOH D:742 , HOH D:922 , HOH D:928 , HOH D:1088
BINDING SITE FOR RESIDUE NAP D 301
12
BC3
SOFTWARE
LEU D:203 , GLY D:207 , ALA D:212 , ASN D:213 , PHE D:216 , ALA D:217
BINDING SITE FOR RESIDUE PEG D 288
13
BC4
SOFTWARE
LEU E:9 , GLY E:10 , ILE E:11 , MET E:12 , ASN E:31 , ARG E:32 , SER E:33 , LYS E:36 , MET E:64 , LEU E:65 , ALA E:66 , ALA E:70 , GLU E:73 , VAL E:74 , THR E:96 , VAL E:121 , GLY E:123 , SER E:124 , ALA E:231 , PHE E:232 , HIS E:236 , LYS E:239 , HOH E:310 , HOH E:317 , HOH E:336 , HOH E:341 , HOH E:481 , HOH E:507 , HOH E:589
BINDING SITE FOR RESIDUE NAP E 301
14
BC5
SOFTWARE
ASP C:204 , GLY C:207 , ALA C:208 , ARG E:32 , SER E:33
BINDING SITE FOR RESIDUE GOL E 288
15
BC6
SOFTWARE
LEU E:203 , GLY E:207 , ALA E:212 , ASN E:213 , ALA E:217
BINDING SITE FOR RESIDUE GOL E 289
16
BC7
SOFTWARE
ALA E:246 , ASP E:249 , HOH E:299 , HOH E:306 , ARG H:242 , HOH H:299
BINDING SITE FOR RESIDUE PEG E 290
17
BC8
SOFTWARE
LEU F:9 , GLY F:10 , ILE F:11 , MET F:12 , ASN F:31 , ARG F:32 , SER F:33 , LYS F:36 , MET F:64 , LEU F:65 , ALA F:66 , ALA F:70 , GLU F:73 , VAL F:74 , THR F:96 , VAL F:121 , GLY F:123 , SER F:124 , ALA F:231 , PHE F:232 , PRO F:233 , HIS F:236 , LYS F:239 , HOH F:297 , HOH F:593 , HOH F:951 , HOH F:1092
BINDING SITE FOR RESIDUE NAP F 301
18
BC9
SOFTWARE
GOL B:288 , LEU G:9 , GLY G:10 , ILE G:11 , MET G:12 , ASN G:31 , ARG G:32 , SER G:33 , MET G:64 , LEU G:65 , ALA G:66 , ALA G:70 , GLU G:73 , VAL G:74 , THR G:96 , VAL G:121 , GLY G:123 , SER G:124 , ALA G:231 , PHE G:232 , HIS G:236 , LYS G:239 , HOH G:309 , HOH G:493 , HOH G:597 , HOH G:638 , HOH G:878 , HOH G:1094
BINDING SITE FOR RESIDUE NAP G 301
19
CC1
SOFTWARE
ARG A:32 , PRO A:34 , HOH A:309 , LEU G:203 , ILE G:206 , GLY G:207 , ALA G:212 , ASN G:213 , PHE G:216 , ALA G:217 , HOH G:435 , HOH G:839
BINDING SITE FOR RESIDUE PEG G 288
20
CC2
SOFTWARE
LEU H:9 , GLY H:10 , ILE H:11 , MET H:12 , ASN H:31 , ARG H:32 , SER H:33 , LYS H:36 , MET H:64 , LEU H:65 , ALA H:66 , ALA H:70 , GLU H:73 , VAL H:74 , THR H:96 , GLY H:123 , SER H:124 , ALA H:231 , PHE H:232 , PRO H:233 , HIS H:236 , LYS H:239 , HOH H:448 , HOH H:508 , HOH H:600 , HOH H:686 , HOH H:1098
BINDING SITE FOR RESIDUE NAP H 301
21
CC3
SOFTWARE
LEU H:203 , ILE H:206 , GLY H:207 , ALA H:212 , ASN H:213 , PHE H:216 , ALA H:217
BINDING SITE FOR RESIDUE PEG H 288
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d3pefa2 (A:163-287)
1b: SCOP_d3pefb2 (B:163-287)
1c: SCOP_d3pefc2 (C:163-287)
1d: SCOP_d3pefd2 (D:163-286)
1e: SCOP_d3pefe2 (E:163-286)
1f: SCOP_d3peff2 (F:163-286)
1g: SCOP_d3pefg2 (G:163-287)
1h: SCOP_d3pefh2 (H:163-287)
2a: SCOP_d3pefa1 (A:1-162)
2b: SCOP_d3pefb1 (B:1-162)
2c: SCOP_d3pefc1 (C:1-162)
2d: SCOP_d3pefd1 (D:1-162)
2e: SCOP_d3pefe1 (E:1-162)
2f: SCOP_d3peff1 (F:2-162)
2g: SCOP_d3pefg1 (G:1-162)
2h: SCOP_d3pefh1 (H:2-162)
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Classes
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)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Geobacter metallireducens [TaxId: 28232]
(1)
1a
d3pefa2
A:163-287
1b
d3pefb2
B:163-287
1c
d3pefc2
C:163-287
1d
d3pefd2
D:163-286
1e
d3pefe2
E:163-286
1f
d3peff2
F:163-286
1g
d3pefg2
G:163-287
1h
d3pefh2
H:163-287
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Geobacter metallireducens [TaxId: 28232]
(1)
2a
d3pefa1
A:1-162
2b
d3pefb1
B:1-162
2c
d3pefc1
C:1-162
2d
d3pefd1
D:1-162
2e
d3pefe1
E:1-162
2f
d3peff1
F:2-162
2g
d3pefg1
G:1-162
2h
d3pefh1
H:2-162
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Sorry, no Info available
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Asym.Unit (734 KB)
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